You are here

Design

output file in ddg calcualtion

Category: 
Design

Hello!

While using ddg_monomer script, I tried flag --ggd:dump_pdbs 'false' and 'true' both, but it is not producing any output pdb file?  any suggestion?

 

"-ddg::dump_pdbs true # write out PDB files for the structures, one for the wildtype and one for the pointmutant for each iteration"

 

Thanks!

Malkeet

Post Situation: 

error for the pose reading:TRP:NtermProteinFull:triazolamerC missing: C1

Category: 
Design

Hi there,

I have a pdb file from CHARMM format. When I use

fixbb.default.linuxgccrelease -in:file:s step1_pdbreader.pdb -in:file:fullatom -resfile resfile_2 -ex1 -ex2 -extrachi_cutoff 1 -nstruct 50 >out

I got this:

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms:    1 A TRP TRP:NtermProteinFull:triazolamerC
core.io.pose_from_sfr.PoseFromSFRBuilder: missing:  CT1


and it skipped the first residue TRP.

Post Situation: 

RosettaRemodel: ERROR: 'Replacing' an atom which doesn't currently exist.

Category: 
Design

Hello!

I am trying to truncate a CDR loop using remodel. I have previously used Rosetta version 58825.2016 (Score function:talaris2014)  successful.

However I recently switched to rosetta weekly release: 

"version": "rosetta.source.release-156", "week": 43,  "year": 2017

And I am getting this error 

protocols.forge.remodel.RemodelWorkingSet: (1) normal rebuild

core.kinematics.tree.Atom_: (1) [ FATAL ] old_atom not present in atoms list! 1

Post Situation: 

terminal amino acids of gap has incomplete valency

Category: 
Design

Hello!

While doing protein minimization, I found that the terminal amino acids of gap (let say 80 and 110) have incomplete valency e.g. -C(O) and -NH instead of -C(O)O-/H and NH2/H+ as rosetta consider them very neighbours during renumbering step. 

I tried modifying both residues (let say 80 and 110) in different protein visualization plateforma and fed to Rosetta, but it modifies them to -C(O) and -NH. 

Could you suggest how to deal with it?

Post Situation: 

rosetta.core.pack.pack_rotamers_setup(pose, score_fxn, task_design, rotsets) not working

Category: 
Design

Dear all,

I have recently upgraded to the newest PyRosetta version (156) because my machine was upgraded to Unbuntu Artful, that uses Python 3.6 (and 144 was compiled for 3.5).

My packing script worked fine in the previous PyRosetta version I used (144) but now fails on rosetta.core.pack.pack_rotamers_setup with the following message.

Post Situation: 

This element is not expected.

Category: 
Design

I am trying to replicate the work of the paper: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature23912.html?foxtrotcallback=true

It seems the Rosetta Script in the supplimentary meterials is old because when I try to use it I get a lot of typo errors, anyway I changed it but I could not find a way to fix this error:

Post Situation: 

Allow region of protein to move in a certain direction

Category: 
Design

Hi,

I have a protein structure. I want to move a specified region (say residues x to y) of this protein in a any direction (more like a dynamic simulation). Is there a protocol that allows this in Rosetta? I have tried the backrub, relax with constraints.

Post Situation: 

Pages

Subscribe to RSS - Design